BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716422.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,568,182 number of mapped reads = 1,452,772 (92.64%) number of supplementary alignments = 5,138 (0.33%) number of secondary alignments = 0 number of mapped bases = 84,780,436 bp number of sequenced bases = 84,753,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,517 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7104 >>>>>>> ACTG content number of A's = 20,772,585 bp (24.51%) number of C's = 17,281,227 bp (20.39%) number of T's = 25,930,762 bp (30.6%) number of G's = 20,767,599 bp (24.5%) number of N's = 1,788 bp (0%) GC percentage = 44.89% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 422,331 number of insertions = 6,283 mapped reads with insertion percentage = 0.43% number of deletions = 16,384 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 0.2629X There is a 2.47% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7158225 0.028718985618896412 0.41674789845491855 chr2 243199373 6692637 0.027519137559618625 0.36855826106355327 chr3 198022430 4852940 0.024507021755060778 0.17042636933024574 chr4 191154276 5220319 0.027309454484816233 0.21135827956988965 chr5 180915260 4805804 0.02656383988835436 0.1768250569514421 chr6 171115067 4505261 0.02632883871062038 0.2049384890074017 chr7 159138663 4789258 0.030094873927651384 0.3312145102295135 chr8 146364022 4484070 0.030636422385277168 0.3533381166027705 chr9 141213431 2803048 0.019849726617009966 0.18497452632833278 chr10 135534747 3698575 0.027288758653159252 0.2716300774379436 chr11 135006516 3010552 0.02229930887187697 0.2049062460434256 chr12 133851895 4182043 0.0312438086887003 0.19226149880560403 chr13 115169878 2543551 0.02208521050964385 0.16207134741340268 chr14 107349540 2846082 0.026512288734539525 0.17895999819996128 chr15 102531392 3147960 0.03070240185561901 0.19106062339605404 chr16 90354753 2940198 0.03254060137821416 0.20578858567737085 chr17 81195210 3679790 0.04532028428770613 0.24080144326147992 chr18 78077248 1562376 0.020010643817773906 0.31769730265525187 chr19 59128983 2162617 0.03657456783926082 0.3237262845618652 chr20 63025520 2841516 0.045085165501212845 0.2408619751380757 chr21 48129895 1102649 0.022909856753271538 0.20594637608733593 chr22 51304566 785800 0.0153163755444301 0.13377756433844107 chrMT 16571 58734 3.544384768571601 2.6765413438407477 chrX 155270560 4589771 0.029559827696892443 0.19941153194213582 chrY 59373566 316660 0.005333349861451812 0.23417070847970065